scPDB - 4dd8 entry

Protein Data Bank Entry:

PDB ID : 4dd8

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2012-01-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Disintegrin and metalloproteinase domain-containing protein 8
ID:	ADAM8_HUMAN
AC:	P78325
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24

Chains:

Chain Name:	Percentage of Residues within binding site
A	19 %
D	81 %

Ligand binding site composition:

B-Factor:	24.966
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	CL ZN

Cavity properties

Ligandability	Volume (Å3)
0.745	880.875

% Hydrophobic	% Polar
32.57	67.43
According to VolSite

Ligand :

HET Code:	BAT
Formula:	C23H31N3O4S2
Molecular weight:	477.640 g/mol
DrugBank ID:	DB03880
Buried Surface Area:	64.59 %
Polar Surface area:	161.07 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
39.2707	-9.31741	12.1498

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C20	CG	GLN- 255	3.83	0	Hydrophobic	false
C22	CD	ARG- 257	3.3	0	Hydrophobic	false
N3	O	THR- 299	2.6	171.22	H-Bond (Ligand Donor)	false
S2	CG2	THR- 300	3.66	0	Hydrophobic	false
C3	CG2	THR- 300	4.44	0	Hydrophobic	false
O3	N	VAL- 301	2.91	159.04	H-Bond (Protein Donor)	false
C10	CG2	VAL- 301	4.1	0	Hydrophobic	false
N1	O	GLY- 302	2.92	161.96	H-Bond (Ligand Donor)	false
S1	CE1	PHE- 303	3.88	0	Hydrophobic	false
C12	CB	THR- 331	4.3	0	Hydrophobic	false
C12	CB	HIS- 334	4.11	0	Hydrophobic	false
N2	O	GLY- 366	3.16	177.28	H-Bond (Ligand Donor)	false
O4	N	ILE- 368	3	164.18	H-Bond (Protein Donor)	false
C10	CG1	ILE- 368	4.02	0	Hydrophobic	false
O1	ZN	ZN- 1002	2.14	0	Metal Acceptor	false
O2	ZN	ZN- 1002	2.17	0	Metal Acceptor	false